=================================== Release notes for DIPY version 1.5 =================================== GitHub stats for 2021/05/06 - 2022/03/10 (tag: 1.4.1) These lists are automatically generated, and may be incomplete or contain duplicates. The following 22 authors contributed 573 commits. * Ariel Rokem * Dan Bullock * David Romero-Bascones * Derek Pisner * Eleftherios Garyfallidis * Eric Larson * Francis Jerome * Francois Rheault * Gabriel Girard * Giulia Bertò * Javier Guaje * Jon Haitz Legarreta Gorroño * Joshua Newton * Kenji Marshall * Leevi Kerkela * Leon Weninger * Lucas Da Costa * Nasim Anousheh * Rafael Neto Henriques * Sam Coveney * Serge Koudoro * Shreyas Fadnavis We closed a total of 200 issues, 72 pull requests and 128 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (72): * :ghpull:`2561`: [FIX] Motion correction tutorial * :ghpull:`2520`: Resdnn inference * :ghpull:`2558`: BUG: Fix errant warning about starting_affine * :ghpull:`2557`: MAINT: Fix version * :ghpull:`2556`: [FIX] Update `dipy.segment` tutorials * :ghpull:`2554`: Support .vtp files * :ghpull:`2555`: Limit `peaks_from_model` number of processes in examples * :ghpull:`2539`: Adds utilities for embarassingly parallel loops. * :ghpull:`2545`: Stateful Tractogram DPS and DPP keys ordering * :ghpull:`2548`: Add timeout + concurrency to GHA * :ghpull:`2549`: [ENH] Clarify reconst_sh tutorial * :ghpull:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow * :ghpull:`2551`: [MNT] Update mininal dependencies version * :ghpull:`2536`: Random colors fix in horizon * :ghpull:`2533`: [FIX] Docstring cleaning: wrong underline length... * :ghpull:`2342`: NF: q-space trajectory imaging * :ghpull:`2512`: Masking for affine registration * :ghpull:`2526`: TEST: Filter legacy SH bases warnings in tests * :ghpull:`2534`: TEST: Remove unnecessary `main` method definition in tests * :ghpull:`2532`: STYLE: Remove unused import statements * :ghpull:`2529`: STYLE: Remove unused import statements * :ghpull:`2528`: TEST: Remove legacy `nose`-related dead testing code * :ghpull:`2527`: TEST: Fix intermittent RUMBA test check failure * :ghpull:`2493`: Fury dependency resolution * :ghpull:`2522`: ENH: Miscellaneous cleanup * :ghpull:`2521`: DOC: Use GitHub actions status badge in README * :ghpull:`2420`: Documentation corrections * :ghpull:`2482`: ENH: Improve SH bases warning messages * :ghpull:`2423`: NF: rumba reconst * :ghpull:`2518`: Migrations from Azure Pipeline to Github Actions * :ghpull:`2515`: Default to False output for null streamlines in streamline_near_roi * :ghpull:`2513`: [MNT] Drop distutils * :ghpull:`2506`: Horizon FURY update * :ghpull:`2510`: Optimize sfm (reboot) * :ghpull:`2487`: ENH: Better error message * :ghpull:`2442`: [NF] Add Motion correction workflow * :ghpull:`2470`: Add utilities functions: radius curvature <--> maximum deviation angle * :ghpull:`2485`: DOC: Small updates. * :ghpull:`2481`: ENH: Import ABCs from `collections.abc` * :ghpull:`2480`: STYLE: Make `sklearn` import warning messages consistent * :ghpull:`2478`: ENH: Deal appropriately with user warnings * :ghpull:`2479`: STYLE: Improve style in misc files * :ghpull:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings * :ghpull:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning * :ghpull:`2472`: ENH: Return unique invalid streamline removal indices * :ghpull:`2471`: DOC: Fix coding style guideline link * :ghpull:`2468`: [MNT] Use windows-latest on azure pipeline * :ghpull:`2467`: [ENH] Add fit_method option in DTI and DKI CLI * :ghpull:`2466`: deprecate dipy.io.bvectxt module * :ghpull:`2453`: make it compatible when number of volume is 2 * :ghpull:`2413`: Azure pipeline: from ubuntu 1604 to 2004 * :ghpull:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors * :ghpull:`2444`: [DOC] : Added citation for IVIM dataset * :ghpull:`2434`: MAINT: Update import from ndimage * :ghpull:`2435`: BUG: Backward compat support for pipeline * :ghpull:`2436`: MAINT: Bump tolerance * :ghpull:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py` * :ghpull:`2374`: ROIs visualizer * :ghpull:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling * :ghpull:`2417`: OPT: Initialize `Shape` struct * :ghpull:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols' * :ghpull:`2406`: Manage Approx_polygon_track with repeated points * :ghpull:`2411`: [FIX] `c_compress_streamline` discard identical points * :ghpull:`2416`: OPT: Prefer using a typed index to get the PMF value * :ghpull:`2415`: Implementation multi_voxel_fit progress bar * :ghpull:`2410`: [ENH] Improve Shore Tests * :ghpull:`2409`: NF - Sample PMF for an input position and direction * :ghpull:`2405`: Small correction on KFA * :ghpull:`2407`: from random to deterministic test for deform_streamlines * :ghpull:`2392`: Add decomposition * :ghpull:`2389`: [Fix] bundles_distances_mdf asymmetric values * :ghpull:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline. Issues (128): * :ghissue:`2561`: [FIX] Motion correction tutorial * :ghissue:`2123`: WIP: Residual Deep NN * :ghissue:`2520`: Resdnn inference * :ghissue:`2558`: BUG: Fix errant warning about starting_affine * :ghissue:`2557`: MAINT: Fix version * :ghissue:`2489`: MAINT: Get Python 3.10 binaries up on scipy-wheels-nightly * :ghissue:`2556`: [FIX] Update `dipy.segment` tutorials * :ghissue:`2554`: Support .vtp files * :ghissue:`2525`: Support Opening `.vtp` files * :ghissue:`2555`: Limit `peaks_from_model` number of processes in examples * :ghissue:`2539`: Adds utilities for embarassingly parallel loops. * :ghissue:`2509`: Easy robustness for streamline_near_roi and near_roi for empty streamlines? * :ghissue:`2543`: StatefulTractogram.are_compatible compare data_per_point keys as list instead of set * :ghissue:`2545`: Stateful Tractogram DPS and DPP keys ordering * :ghissue:`2548`: Add timeout + concurrency to GHA * :ghissue:`2549`: [ENH] Clarify reconst_sh tutorial * :ghissue:`2546`: Confusing import in 'reconst_sh` * :ghissue:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow * :ghissue:`2542`: DTI workflow should allow user-defined fitting method * :ghissue:`2551`: [MNT] Update mininal dependencies version * :ghissue:`2477`: Numpy min dependency update * :ghissue:`2541`: Issue with coverage and pytests for numpy.min() * :ghissue:`2507`: kernel died when use dipy.viz * :ghissue:`2536`: Random colors fix in horizon * :ghissue:`2533`: [FIX] Docstring cleaning: wrong underline length... * :ghissue:`2422`: WIP-Adding math in SLR tutorial * :ghissue:`2342`: NF: q-space trajectory imaging * :ghissue:`2512`: Masking for affine registration * :ghissue:`1969`: imaffine mask support * :ghissue:`2526`: TEST: Filter legacy SH bases warnings in tests * :ghissue:`2456`: Horizon tests failing * :ghissue:`2534`: TEST: Remove unnecessary `main` method definition in tests * :ghissue:`2532`: STYLE: Remove unused import statements * :ghissue:`2524`: Add concurrency + timeout to Github Actions (GHA) * :ghissue:`2529`: STYLE: Remove unused import statements * :ghissue:`2528`: TEST: Remove legacy `nose`-related dead testing code * :ghissue:`2527`: TEST: Fix intermittent RUMBA test check failure * :ghissue:`2493`: Fury dependency resolution * :ghissue:`2522`: ENH: Miscellaneous cleanup * :ghissue:`2521`: DOC: Use GitHub actions status badge in README * :ghissue:`2420`: Documentation corrections * :ghissue:`2482`: ENH: Improve SH bases warning messages * :ghissue:`2449`: Nonsense deprecation warning * :ghissue:`2423`: NF: rumba reconst * :ghissue:`2179`: NF: Complete masking implementation in affine registration with MI * :ghissue:`2518`: Migrations from Azure Pipeline to Github Actions * :ghissue:`2492`: Move to GitHub actions / reusable actions * :ghissue:`2515`: Default to False output for null streamlines in streamline_near_roi * :ghissue:`2497`: Remove python 3.6 from Azure pipelines * :ghissue:`2495`: Remove Distutils (deprecated) * :ghissue:`2513`: [MNT] Drop distutils * :ghissue:`2506`: Horizon FURY update * :ghissue:`2305`: [WIP] Brain Tumor Image Segmentation Code * :ghissue:`2499`: Problem generating Connectivity Matrix: "Slice step cannot be zero" * :ghissue:`2510`: Optimize sfm (reboot) * :ghissue:`2488`: Minimize memory footprint whereever possible, add joblib support for … * :ghissue:`2504`: Why are there many small dots on the fwdwi image? * :ghissue:`2502`: Can i read specific b-values from my own multishell data? * :ghissue:`2500`: MAP issue * :ghissue:`2490`: [BUG] MRI-CT alignment failure * :ghissue:`2487`: ENH: Better error message * :ghissue:`2402`: Dipy 1.4.1 breaks nipype.interfaces.dipy.dipy_to_nipype_interface * :ghissue:`2486`: Wrong doc in interpolation * :ghissue:`2442`: [NF] Add Motion correction workflow * :ghissue:`2470`: Add utilities functions: radius curvature <--> maximum deviation angle * :ghissue:`2485`: DOC: Small updates. * :ghissue:`2484`: [ENH] Add grid search to `AffineRegistration.optimize` * :ghissue:`2483`: [DOC] Stable/Latest Documentation Structure * :ghissue:`2481`: ENH: Import ABCs from `collections.abc` * :ghissue:`2480`: STYLE: Make `sklearn` import warning messages consistent * :ghissue:`2478`: ENH: Deal appropriately with user warnings * :ghissue:`2479`: STYLE: Improve style in misc files * :ghissue:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings * :ghissue:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning * :ghissue:`2472`: ENH: Return unique invalid streamline removal indices * :ghissue:`2471`: DOC: Fix coding style guideline link * :ghissue:`2468`: [MNT] Use windows-latest on azure pipeline * :ghissue:`2467`: [ENH] Add fit_method option in DTI and DKI CLI * :ghissue:`2463`: DTI RESTORE on the CLI * :ghissue:`2466`: deprecate dipy.io.bvectxt module * :ghissue:`2460`: Deprecate and Remove dipy.io.bvectxt * :ghissue:`2429`: random_colors flag in dipy_horizon does not work as before * :ghissue:`2461`: Patch2Self: Less than 10 3D Volumes Bug * :ghissue:`2464`: Typo on the homepage * :ghissue:`2453`: make it compatible when number of volume is 2 * :ghissue:`2457`: Choosing sigma_diff and radius parameters for SyN registration * :ghissue:`2413`: Azure pipeline: from ubuntu 1604 to 2004 * :ghissue:`2454`: Can I show fiber with vtk? * :ghissue:`2446`: Use of bitwise or with non-bool inputs results in ufunc 'bitwise_or' error * :ghissue:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors * :ghissue:`2444`: [DOC] : Added citation for IVIM dataset * :ghissue:`2443`: Citation for IVIM dataset not present in docs * :ghissue:`2434`: MAINT: Update import from ndimage * :ghissue:`2441`: Horizon error - disk position outside the slider line * :ghissue:`2435`: BUG: Backward compat support for pipeline * :ghissue:`2436`: MAINT: Bump tolerance * :ghissue:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py` * :ghissue:`2430`: dipy.align.reslice * :ghissue:`2431`: dipy.align.reslice interpolation order for downsampling * :ghissue:`2432`: How to apply MI metric in dipy？ * :ghissue:`2374`: ROIs visualizer * :ghissue:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling * :ghissue:`2417`: OPT: Initialize `Shape` struct * :ghissue:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols' * :ghissue:`2406`: Manage Approx_polygon_track with repeated points * :ghissue:`2314`: Approx_polygon_track with repeated points gives an error * :ghissue:`2411`: [FIX] `c_compress_streamline` discard identical points * :ghissue:`1805`: `c_compress_streamline` keeps identical points when it shouldn't * :ghissue:`2418`: kernel failure when importing mask from dipy.segment * :ghissue:`2416`: OPT: Prefer using a typed index to get the PMF value * :ghissue:`2415`: Implementation multi_voxel_fit progress bar * :ghissue:`2410`: [ENH] Improve Shore Tests * :ghissue:`365`: Code review items for `dipy.reconst.shore` * :ghissue:`2409`: NF - Sample PMF for an input position and direction * :ghissue:`2404`: Change affine in StatefulTractogram * :ghissue:`2405`: Small correction on KFA * :ghissue:`2407`: from random to deterministic test for deform_streamlines * :ghissue:`2392`: Add decomposition * :ghissue:`717`: Download each shell of the CENIR data separately? * :ghissue:`2209`: _pytest.pathlib.ImportPathMismatchError: * :ghissue:`1934`: Random lpca denoise * :ghissue:`2312`: DIPY open group meetings, Spring 2021 * :ghissue:`2383`: error in mcsd model fitting (DCPError) * :ghissue:`2391`: error performing cross-validation on diffusion HCP data * :ghissue:`2393`: Add a function to read streamline from the result generated by the command "probtrackx2" in FMRIB's Diffusion Toolbox * :ghissue:`2389`: [Fix] bundles_distances_mdf asymmetric values * :ghissue:`2310`: `bundles_distances_mdf` asymmetric values * :ghissue:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.